Skip to Content
Last modified by chatzies on 2025-11-27 11:35
From version 1.1
edited by ahenkel
on 2021-11-30 10:29
Change comment: There is no comment for this version
To version 83.6
edited by tabermah
on 2024-12-10 15:54
Change comment: There is no comment for this version

Summary

Details

Page properties
Title
... ... @@ -1,1 +1,1 @@
1 -Serial Crystallography: CFEL TapeDrive
1 +08. Serial Crystallography: CFEL TapeDrive
Author
... ... @@ -1,1 +1,1 @@
1 -XWiki.ahenkel
1 +XWiki.tabermah
Content
... ... @@ -1,0 +1,396 @@
1 +{{layout}}
2 +{{layout-section ac:type="single"}}
3 +{{layout-cell}}
4 +[[image:attach:TapeDrive_beschriftet-tile.jpg||height="400"]]
5 +
6 +
7 +{{toc/}}
8 +
9 +
10 +----
11 +
12 += {{id name="14.SerialCrystallography:CFELTapeDrive-14.1Samplecharacteristicsandpreparation"/}}8.1. Sample characteristics and preparation =
13 +
14 +* Suspension of microcrystals, **at least** 200 µL with 20% crystal density (more is always better), size range: 2-30 µm, **tip:** bring some mother liquor for washing, filtering, diluting etc.
15 +
16 +Preparation:
17 +
18 +* filter through 30 µm (green) or 50 µm (yellow) cell filter into an Eppendorf or Falcon (original!) tube
19 +
20 +[[image:attach:20211201_095534.jpg||height="250"]]
21 +
22 +
23 +----
24 +
25 += {{id name="14.SerialCrystallography:CFELTapeDrive-14.2ConnectingsampletoElveFlow,sampleexchange"/}}8.2. Connecting sample to ElveFlow, sample exchange =
26 +
27 +After filtration, screw the ElveFlow connector to your Eppendorf or Falcon tube. Make sure that the yellow-ish tube goes all the way to the bottom of your tube. You can adjust the length by unscrewing the blue fitting on top and pushing/pulling the yellow-ish line. **Don't forget to tigthen the blue fitting afterwards!**
28 +
29 +Be aware to which channel and nozzle line your sample is connected.
30 +
31 + Red → Channel 1, crystal line (nozzle capillary without marks/with red marks)
32 +
33 + Green → Channel 2, substrate line (nozzle capillary is marked in black)
34 +
35 +[[image:attach:20211201_095033.jpg||thumbnail="true" height="250"]]
36 +
37 +After finishing data collection, flush all lines by connecting an Eppi or syringe filled with ddH,,2,,O.
38 +
39 +[[image:attach:20211201_095232.jpg||height="250"]][[image:attach:20211201_095205.jpg||height="250"]]
40 +
41 +
42 +----
43 +
44 += {{id name="14.SerialCrystallography:CFELTapeDrive-14.3TapeDriveoperation"/}}8.3. TapeDrive operation =
45 +
46 +​​​​​​The TapeDrive is controlled through kamzik. To open kamzik, start the server. A terminal will open and shortly after a small window.
47 +
48 +Now start the client. Same thing, a terminal will open, shortly after a small window.
49 +
50 +Click 'Devices' in the **client session** to open the control window.
51 +[[image:attach:screen.PNG||height="250"]][[image:attach:server client.PNG||height="250"]]
52 +
53 +== {{id name="14.SerialCrystallography:CFELTapeDrive-Tape"/}}Tape ==
54 +
55 +* Click the 'main tape' icon
56 +* Change the velocity by typing anything from **0.3-3.0 mm/s**
57 +* Common velocity is 1.0-1.5 mm/s
58 +* kamzik displays the used tape in m and %. At 98% the tape will automatically stop since the rolls need to be exchanged at this point.
59 +
60 +
61 +[[image:attach:kamzik_tape.PNG||height="400"]]
62 +
63 +
64 +== {{id name="14.SerialCrystallography:CFELTapeDrive-Samplenozzle"/}}Sample nozzle ==
65 +
66 +* Click on the 'nozzle' icon.
67 +* (((
68 +The nozzle position can be adjusted in xyz by clicking on the arrows up and down. (Double arrow = 10 steps). Step size can be varied, 1mm steps are rather big and should be used carefully.
69 +The absolute position is **not calibrated** and therefore changes after each restart of kamzik.
70 +
71 +
72 +(% style="color:#ff0000" %)**!!! **(% style="color:#000000" %)**During data collection make sure in which direction you are moving the nozzle, do not move nozzle into beam**(% style="color:#ff0000" %)** !!!**(%%)
73 +\\Adjust the nozzle position by eye until it nearly touches the tape and roughly meets the X-ray interaction point. Then, move to the control hutch to use the on-axis microscope for fine adjustment. Move the nozzle tip to the beam position (red X) and write down the absolut nozzle position. From there move the nozzle in +x to your desired distance.Different distances combined with the tape speed result in several delay times for time-resolved experiments.
74 +
75 +(% class="wrapped" %)
76 +|=(((
77 +
78 +)))|=(((
79 +direction
80 +)))|=(((
81 +recommended step size
82 +for visual adjustment
83 +)))|=(% colspan="1" %)(((
84 +recommended step size
85 +during data collection
86 +)))
87 +|(((
88 ++x
89 +)))|(((
90 +away from X-ray interaction point
91 +)))|(((
92 +1.0 - 0.5 mm
93 +)))|(% colspan="1" %)(((
94 +0.1 - 0.2 mm
95 +)))
96 +|(((
97 ++y
98 +)))|(((
99 +up
100 +)))|(((
101 +1.0 - 0.5 mm
102 +)))|(% colspan="1" %)(((
103 +0.1 - 0.2 mm
104 +)))
105 +|(((
106 ++z
107 +)))|(((
108 +towards detector tower, away from tape
109 +)))|(((
110 +0.5 - 0.2 mm
111 +)))|(% colspan="1" %)(((
112 +0.1 - 0.2 mm
113 +be careful with -z, tape could be pushed out of focus
114 +)))
115 +
116 +
117 +)))
118 +
119 +[[image:attach:kamzik_nozzle.PNG||height="400"]]
120 +
121 +
122 +== {{id name="14.SerialCrystallography:CFELTapeDrive-Temperaturecontrol/Chiller"/}}Temperature control/Chiller ==
123 +
124 +* The chiller circulates fluid through the gas nozzle.
125 +
126 +== {{id name="14.SerialCrystallography:CFELTapeDrive-Gasnozzle"/}}Gas nozzle ==
127 +
128 +
129 +== {{id name="14.SerialCrystallography:CFELTapeDrive-IRcamera"/}}IR camera ==
130 +
131 +
132 +Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
133 +
134 + xfreerdp +clipboard /size:1920x1080 /u:Cfelusr /v:cfeld-pcx22611
135 + password: //written on control laptop (changes every 6 months)//
136 +
137 +
138 +
139 +----
140 +
141 += {{id name="14.SerialCrystallography:CFELTapeDrive-14.4Taperollexchange"/}}8.4. Tape roll exchange =
142 +
143 +The tape stops automatically at 98% used length, if you need to change the rolls for orther reasons, stop the tape (velocity = 0.0 mm/s).
144 +
145 +* Remove the (almost) empty feeder roll by pulling it upwards.
146 +* Cut the tape with some cm overlap to glue to the new roll. **Do not discard empty roll!**
147 +* Get a new tape roll (bottom left on the cart). **Polypropylen 15 µm**
148 +* Cut the first cm of the new tape roll, directly behind the black sticky part.
149 +* Place new roll on roll holder and use sticky tape to attach the end of the old tape to the beginning of the new roll.
150 +* Open magnetic tape stabilizer on the **left side**. (% style="color:#ff0000" %)//!!!BEAMSTOP!!!//
151 +* Start the tape (3mm/s). Once the connetion side has arrived at the collector roll, stop the tape (0mm/s).
152 +* Again, cut the tape directly behind the connection side. Replace the the old roll with the **empty **one. Old roll can be discarded.
153 +* Attach new tape to the empty roll by using some sticky tape.
154 +* Close tape stabilizer.
155 +* Reset tape counter in kamzik by clicking "<Call>" in "Main-Tape".
156 +
157 +**[[image:attach:20211201_094101.jpg||height="250"]][[image:attach:20211201_094111.jpg||height="250"]][[image:attach:tape reset.PNG||height="250"]]**
158 +
159 +
160 +{{/layout-cell}}
161 +{{/layout-section}}
162 +
163 +{{layout-section ac:type="single"}}
164 +{{layout-cell}}
165 +----
166 +
167 += {{id name="14.SerialCrystallography:CFELTapeDrive-14.5Chopper"/}}8.5. Chopper =
168 +
169 +start chopper gui from terminal:
170 +
171 +(% class="code" %)
172 +(((
173 + cd /gpfs/local/shared/ChopperControl          
174 +)))
175 +
176 +(% class="code" %)
177 +(((
178 + python chopperControl.py
179 +\\
180 +)))
181 +{{/layout-cell}}
182 +{{/layout-section}}
183 +
184 +{{layout-section ac:type="two_equal"}}
185 +{{layout-cell}}
186 + [[image:attach:20211212_233140.jpg||height="250"]]
187 +{{/layout-cell}}
188 +
189 +{{layout-cell}}
190 +**Chopper → no Chopper**
191 +
192 +* decrease frequency by max. 10 Hz steps
193 +** click arrow down 10x, "Set", arrow down 10x, "Set", ....
194 +* at frequency = 10 Hz, click "Stop"
195 +* set "Hole" to <none> (% style="color:#ff0000" %)//Takes some minutes//
196 +
197 +(% style="color:#000000" %)**no Chopper → Chopper**
198 +
199 +* (% style="color:#000000" %)set "Hole" to <Inner hole (largest)> (% style="color:#ff0000" %)//Takes some minutes//
200 +* (% style="color:#000000" %)increase frequency by max. 10 Hz steps
201 +** (% style="color:#000000" %)click arrow up 10x, "Set", arrow up 10x, "Set", .....
202 +* (% style="color:#000000" %)//usually 130 Hz, results in exposure time of 3.7 ms (technical exposure will always be 7.7 ms, since max. frame rate is 130 Hz//
203 +{{/layout-cell}}
204 +{{/layout-section}}
205 +
206 +{{layout-section ac:type="single"}}
207 +{{layout-cell}}
208 +----
209 +
210 += {{id name="14.SerialCrystallography:CFELTapeDrive-14.6Datacollection"/}}8.6. Data collection =
211 +
212 +Once the hutch is interlocked, set remote control to the TapeDrive laptop by opening a terminal and executing the following command:
213 +
214 +(% class="code" %)
215 +(((
216 + xfreerdp +clipboard /size:1920x1080 /u:cfelusr /v:cfeld-tapetop
217 + password: written on control laptop (changes every 6 months)
218 +)))
219 +
220 + //>>usually the terminal is open, just repeat previous command with arrow up, enter and type in the password//
221 +
222 +
223 +{{/layout-cell}}
224 +{{/layout-section}}
225 +
226 +{{layout-section ac:type="two_left_sidebar"}}
227 +{{layout-cell}}
228 +**Check list:**
229 +
230 +(% style="color:#ff0000" %)//always after entering the hutch!//
231 +
232 +(% style="color:#000000" %)Click "Run" icon in kamzik.
233 +
234 +* Put detector distance 200 mm in //prepare_for_measurement (      )//
235 +* Click "<Call>" next to //prepare_for_measurement//
236 +This will:
237 +** drive the collimator in //IN// position
238 +** drive detector to 200 mm
239 +
240 +* Open beam shutter BS1 in //CrystalControl //or// P11 XRayFeed //
241 +
242 +//**Set run parameters and go 🏃💥**//
243 +
244 +1. Set your desired No. of frames
245 +1. Enter the protein ID of your crystal sample
246 +1. Match exposure time with chopper setting or set desired exposure time
247 +1. Check trigger setting and match to chopper setting
248 +no chopper → external triffer //off//
249 + chopper → external trigger// on//
250 +1. To start the run, click "<Call>" next to //start_run (exposure    )//
251 +{{/layout-cell}}
252 +
253 +{{layout-cell}}
254 +[[image:attach:Kamzik_run(2).PNG]]
255 +{{/layout-cell}}
256 +{{/layout-section}}
257 +
258 +{{layout-section ac:type="single"}}
259 +{{layout-cell}}
260 +(% class="relative-table wrapped" style="width:55.9569%" %)
261 +|=(((
262 +Parameter
263 +)))|=(((
264 +explanation
265 +)))|=(% colspan="1" %)(((
266 +value
267 +)))
268 +|(((
269 +Images number
270 +)))|(((
271 +number of frames you want to collect
272 +)))|(% colspan="1" %)(((
273 +usually 100k - 200k, but adjust according to hitrate
274 +
275 +orientation: 10 % hitrate needs at least 100k images
276 +)))
277 +|(((
278 +exposure
279 +)))|(((
280 +exposure time of Eiger
281 +
282 +
283 +)))|(% colspan="1" %)(((
284 +with chopper         → opening time displayed in chopper GUI
285 +no chopper            → 7.7 ms
286 +
287 +----
288 +)))
289 +|(((
290 +run id
291 +)))|(((
292 +changes automatically
293 +)))|(% colspan="1" %)(((
294 +
295 +)))
296 +|(% colspan="1" %)(((
297 +Detector distance
298 +)))|(% colspan="1" %)(((
299 +current detector postion readout
300 +)))|(% colspan="1" %)(((
301 +
302 +)))
303 +|(% colspan="1" %)(((
304 +protein ID
305 +)))|(% colspan="1" %)(((
306 +protein ID of crystal sample (see AMARCORD)
307 +)))|(% colspan="1" %)(((
308 +
309 +)))
310 +
311 +----
312 +{{/layout-cell}}
313 +{{/layout-section}}
314 +
315 +{{layout-section ac:type="two_equal"}}
316 +{{layout-cell}}
317 +**After data collection/Before entering the exp. hutch:**
318 +
319 +1. Go to "Safety" in kamzik.
320 +1. Click "<Call>" next to //prepare_to_open_hutch. //This will automatically:
321 +11. Drive the collimator out
322 +11. Drive the detector back to 1500 mm
323 +1. Close beam shutter BS1 and break door interlock in //P11 XRayFeed //(monitor top left).
324 +
325 +[[image:attach:Screenshot from 2022-04-04 19-36-29.png]]
326 +{{/layout-cell}}
327 +
328 +{{layout-cell}}
329 +
330 +
331 +[[image:attach:safety_kamzik.PNG]]
332 +{{/layout-cell}}
333 +{{/layout-section}}
334 +
335 +{{layout-section ac:type="single"}}
336 +{{layout-cell}}
337 +----
338 +
339 += {{id name="14.SerialCrystallography:CFELTapeDrive-14.7Troubleshooting"/}}8.7. Troubleshooting =
340 +
341 +* (((
342 +== {{id name="14.SerialCrystallography:CFELTapeDrive-Tapestopped"/}}Tape stopped ==
343 +
344 +* Tape roll empty?
345 +* motor connected (icon green)?
346 +)))
347 +
348 +* (((
349 +== {{id name="14.SerialCrystallography:CFELTapeDrive-Nozzlemotorsarenotresponding"/}}Nozzle motors are not responding ==
350 +
351 +* displayed in green=connected?
352 +* nozzle holder colliding somewhere?
353 +* motor limits reached? → position displayed in red
354 +)))
355 +
356 +* (((
357 +== {{id name="14.SerialCrystallography:CFELTapeDrive-Sampleflowisnotrespondingtohigherpressure"/}}Sample flow is not responding to higher pressure ==
358 +
359 +* channel turned on?
360 +* Sample empty?
361 +* Nozzle or lines clogged? → flush with water, change nozzle
362 +)))
363 +
364 +* (((
365 +== {{id name="14.SerialCrystallography:CFELTapeDrive-Simplonfilewriter/eigerstreamissues"/}}Simplon filewriter/eiger stream issues ==
366 +
367 +* First, restart kamzik (server+client) and see if this solves the issue
368 +* If not, restart the Simplon server (in Astor → haspp11exp03, right click on Simplon/EH.1 and restart)
369 +* (((
370 +If nothing works, kill the Simplon process and then start the server again:*
371 +
372 +(((
373 +(% class="code" %)
374 +(((
375 +ssh haspp11exp03
376 +)))
377 +)))
378 +
379 +* (((
380 +(% class="code" %)
381 +(((
382 +ps -ef | grep Simplon
383 +)))
384 +)))
385 +* (((
386 +(% class="code" %)
387 +(((
388 +kill -9 simplon_process_id
389 +)))
390 +)))
391 +)))
392 +* After the Simplon server is back up, close all kamzik windows and restart (first server, then client)
393 +)))
394 +{{/layout-cell}}
395 +{{/layout-section}}
396 +{{/layout}}
20211201_094101.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +5.8 MB
Content
20211201_094111.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +5.6 MB
Content
20211201_095033.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +3.1 MB
Content
20211201_095205.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +2.8 MB
Content
20211201_095232.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +7.2 MB
Content
20211201_095534.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +4.4 MB
Content
20211212_233140.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +6.5 MB
Content
Kamzik_run(2).PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +134.4 KB
Content
Screenshot from 2022-04-04 19-36-29.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +133.0 KB
Content
TapeDrive coords.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +24.1 KB
Content
TapeDrive scheme.png
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +114.3 KB
Content
TapeDrive_beschriftet-tile.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +539.9 KB
Content
TapeDrive_beschriftet.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +337.8 KB
Content
kamzik_nozzle.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +120.5 KB
Content
kamzik_run-tile.jpg
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +466.4 KB
Content
kamzik_run.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +128.9 KB
Content
kamzik_safety.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +139.1 KB
Content
kamzik_tape.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +122.6 KB
Content
safety_kamzik.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +126.9 KB
Content
screen.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +94.0 KB
Content
server client.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +262.2 KB
Content
tape reset.PNG
Author
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel
Size
... ... @@ -1,0 +1,1 @@
1 +122.3 KB
Content
Confluence.Code.ConfluencePageClass[0]
Id
... ... @@ -1,1 +1,1 @@
1 -235031814
1 +235031805
Title
... ... @@ -1,1 +1,1 @@
1 -Serial Crystallography: CFEL TapeDrive
1 +14. Serial Crystallography: CFEL TapeDrive
URL
... ... @@ -1,1 +1,1 @@
1 -https://confluence.desy.de/spaces/11/pages/235031814/Serial Crystallography: CFEL TapeDrive
1 +https://confluence.desy.de/spaces/11/pages/235031805/14. Serial Crystallography: CFEL TapeDrive
XWiki.XWikiRights[0]
Allow/Deny
... ... @@ -1,0 +1,1 @@
1 +Allow
Levels
... ... @@ -1,0 +1,1 @@
1 +view,comment,edit
Users
... ... @@ -1,0 +1,1 @@
1 +XWiki.ahenkel